Urban air quality affects the apple microbiome assembly.

Exposure to air pollution affects health of all organisms on earth but the impact on the plant microbiome is less understood. Here, we link the Air Quality Index with the dust and apple epiphytic and endophytic microbiome across the city of Graz (Austria). The microbiome of the apple episphere, peel endosphere and pulp endosphere, and surrounding dust was analyzed. Our results show that the fungal communities were more influenced by air quality than bacterial communities. Bacterial communities, instead, were more specific for the individual sample types, especially noticeable in the pulp endosphere. The microbiome of each sample type was comprised of distinct microbial communities. Overall, the bacterial communities were highly dominated by Proteobacteria followed by Bacteroidota and Actinobacteriota, and the fungal communities were dominated by Ascomycota followed by Basidiomycota. With lower air quality, the relative abundance of the fungal orders Hypocreales and Pleosporales decreased in the apple episphere and the peel endosphere, respectively. Interestingly, an unexpectedly high level of similarity was observed between the bacterial communities of dust and peel endosphere, while the epiphytic bacterial community was significantly different compared to the other samples. We suggested that dust served as a potential microbial colonization route for the fruit microbiome as most bacteria (55%) colonizing the peel endosphere originated from dust. In conclusion, air quality affects the microbiome of edible plants, which can cause health consequences in humans. Therefore, this knowledge should be considered in urban and horticultural farming strategies.